title: Expression of RNA-seq in lesions of a human with tree-man syndrome

city: New York City

first: Franck

last: Rapaport

state: NY

address: 1230 York Ave

institute: Rockefeller University

summary: Two tree-man syndrome lesions immersed in RNA later were snap-frozen in liquid nitrogen and crushed with a tissue pulverizer kit (Cell crusher) according to the manufacturer’s instructions. Total RNA was extracted with the RNeasy Fibrous Tissue Mini Kit (QIAGEN), according to the manufacturer’s instructions. The procedure included a DNAse digestion step or an additional column to remove contaminating DNA. The concentration and purity of the total RNA extracted were measured by spectrometry with an Xpose (Trinean). RNA integrity was evaluated by capillary electrophoresis with a Tape Station (Agilent). The Ovation Universal RNA-Seq System from NUGEN was used to prepare the RNA-seq libraries from100 ng of total RNA, as recommended by the manufacturer. This type of RNAseq kit is less sensitive to total RNA degradation (the RNA integrity number (RIN) of the two samples was quite low: 3.9 for one sample and 5 for the other). This kit constructs strand-specific RNA-seq libraries from 10 to 100 ng of total RNA and uses Insert-Dependent Adaptor Cleavage(InDA-C) technology to remove the ribosomal RNA transcripts. The RNA is subjected to reverse transcription and the second strand is synthesized and a fragmentation step is then performed before Illumina-compatible indexed adaptator ligation. This ligation is followed by a strand-selection enzymatic reaction to provide information about the sense of the transcripts. Insert-dependent adaptor cleavage (InDA-C)-specific primers were then used for the targeted depletion of human ribosomal RNA sequencing transcripts before PCR enrichment. We ensure that no excess amplification occurred during the final PCR step, by evaluating the number of PCR cycles to be applied to each sample in a preliminary Q-PCR test with EvaGreen. An equimolar pool of the final indexed RNA-Seq libraries was sequenced on an Illumina NovaSeq6000 (paired-end reads, 100 bases + 100 bases) and ~50 million paired-end reads per library were produced.

sample_organism:
Homo sapiens
Human papillomavirus type 2

overall_design: Total RNA-seq in two separate warts from the same patient

first: Vivien

last: Beziat


title: Tumor-derived Schwann-like cells promote neuroblastoma survival through secreted trophic factors

status: Public on Aug 11 2021

city: Hong Kong

first: Andrew

middle: M.

last: Chan

address: Room 407, 4/F, Lo Kwee-Seong Integrated Biomedical Sciences Building,, Area 39, The Chinese University of Hong Kong

department: School of Biomedical Science

country: Hong Kong

institute: The Chinese University of Hong Kong

type: Expression profiling by high throughput sequencing

summary: Neuroblastoma (NB) is comprised of a mixture of neuroblastic N-type cancer cells, and Schwannian stromal S-type cells.  Sublines of N- and S-type cells were isolated from an early passage of SK-N-SH NB cell line.  RNA-Seq analysis was conducted on slected N- and S-type cells in order to define their unique expression profiles.

overall_design: An N-type cell line, NC3; and an S-type cell line, S3, was selected. RNA was extracted in duplicate and subjected to RNA-Sequencing analysis.

first: Jing

last: Li

middle: M


title: Integrating Enhancer RNA Signatures with Diverse Omics Data identifies characteristics of transcription initiation in pancreatic islets

city: Ann Arbor

first: Stephen

middle: C. J.

last: Parker

state: MI

address: 100 Washtenaw Ave

department: Computational medicine and Bioinformatics

country: USA

institute: University of Michigan

summary: Identifying active regulatory elements and their characteristics is critical to understand gene regulatory mechanisms and subsequently better delineating biological mechanisms of complex diseases and traits. Studies have shown that active enhancers can be transcribed into enhancer RNA (eRNA). We identified actively transcribed  elements in human pancreatic islets by performing cap analysis of gene expression (CAGE) across 70 islet samples. We used the self-transcribing active regulatory region sequencing (STARR-seq) assay in a rat pancreatic islet beta cell line to experimentally validate the regulatory activity of the CAGE-identified transcribed elements.

sample_organism:
Rattus norvegicus
synthetic construct

platform_organism:
Rattus norvegicus
synthetic construct

overall_design: We selected a total of 7,188 islet CAGE elements (198bp each) to test in the STARR-seq assay. We generated 230-bp synthetic oligos (198bp CAGE element flanked by 16bp anchor sequences, Agilent) and cloned into the STARR-seq backbone plasmid. We inserted 16-bp random nucleotides (‘barcodes’) in the plasmid library using Gibson assembly. We electroporated 10 ug of barcoded STARR-seq library into 25 million the 832/13 rat insulinoma cell line for each of the three biological replicates, and harvested the cells twenty-fours later. We isolated total RNA and purified mRNA using oligo(dT) beads, treated with RNase-free DNaseI and then reverse transcribed it into cDNA. We performed PCR amplification and sequenced the libraries on the Illumina HiSeq platform.

first: Arushi

last: Varshney

first: Yasuhiro

last: Kyono

first: Venkateswaran

middle: R

last: Elangovan

first: Jacob

middle: O

last: Kitzman

middle: C


title: Gene expression signitures in ARPE-19 cells treated with or without TGF-β1

city: Shanghai

first: Shuai

last: Yang

address: 301 Middle Yanchang Road

department: Department of Ophthalmology

country: China

institute: Shanghai Tenth People's Hospital, Tongji University School of Medicine

summary: To identify the dysregulated lncRNA and mRNA expression in ARPE-19 cells underwent EMT, we established a TGF-β1 induced EMT model of ARPE-19 cells. ARPE-19 cells were treated with or without 10 ng/ml TGF-β1 for 48 h. Total RNA are extracted and subjected to microarray assay (Arraystar Human LncRNA Microarray V3.0)

overall_design: ARPE-19 cells treated with or without TGF-β were cultured in triplicates. Three samples of control and three samples of TGF-β1 treated cells are subjected to the microarray assay.

first: Fang

last: Wang


title: RNA demethylation induces increased crop biomass and productivity in the field

city: Chicago

first: Shun

last: Liu

state: IL

address: 929 E. 57th. Street

department: Chemistry

institute: University of Chicago

type: Methylation profiling by high throughput sequencing

summary: We performed the transcriptome-wide m6A profiling (MeRIP) with poly(A) RNA samples isolated from shoots and roots of wild type (Nipp), FTO homogeneous transgenic (FTO) and demethylation activity dead mutant variant of FTO transgenic (FTOmut) rice plants. The m6A motif and the distribution of the detected m6A sites along transcripts were consistent with reported results from previous m6A sequencing studies in plants. We then analyzed the differentially methylated m6A sites in poly(A) RNA species including those transcribed from gene loci and from repetitive elements (repeat RNAs). Compared to Nipp plants, both shoots and roots of FTO transgenic plants had showed more hypomethylated m6A peaks (hypo-m6A, 222 in shoots and 3313 in roots) than hypermethylated m6A peaks (hyper-m6A, 63 in shoots and 127 in roots) in mRNAs, while FTOmut rice had showed more hyper-m6A in shoots (349 for hyper vs 31 for hypo) but more hypo-m6A in roots (291 for hyper vs 380 for hypo) than the WT. The hypomethylated m6A peaks in FTO transgenic plants were highly enriched within 3'UTR. Gene Ontology (GO) analysis of these identified hypomethylated m6A-containing coding genes in both FTO transgenic rice shoots and roots revealed an enrichment for functional annotations related to “cellular homeostatic process”, “one-carbon and small molecule metabolic process”, and “gene expression”. We also found the extent of m6A hypomethylation was more pronounced for repeat RNAs than for mRNA species.The quantitative RNA-seq analysis that included ERCC spike-in controls confirmed that FTO plants do indeed accumulate higher overall levels of poly(A) RNA than do WT shoots and roots. Above all, FTO mediated m6A demethylation in plant mRNA and repeats RNA, leading to the activation of transcription.

overall_design: Gene expression and m6A peaks were identified from RNA-seq and m6A-seq data, respectively. Both types of data were from the shoots and roots of wild type, FTO homogeneous transgenic and demethylation activity dead mutant variant of FTO homogeneous transgenic rice in two replicates.

first: Qiong

last: Yu

first: Chuan

last: He

first: Guifang

last: Jia


title: RNA Sequencing facilitates quantitative Analysis of differently expressed genes with negative control (NC) and siLINK-A treatment in rheumatoid fibroblast-like synoviocytes

status: Public on Aug 10 2021

city: Guangzhou

first: Jingnan

state: Guangdong

address: Zhongshan 2nd Road

institute: Department of Rheumatology and Immunology, The First Affiliated Hospital, Sun  Yat-sen University

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Single cell RNA analysis of trunk neural crest cells in zebrafish

city: Easton

first: Ezra

last: Lencer

state: PA

address: 746 High Street

department: Department of Biology

institute: Lafayette College

summary: Single cell RNA-seq data of tg(sox10:GFP) cells from 20-24 hours post fertilization zebrafish. Sequenced with 10x genomics.

overall_design: tg(sox10:GFP) cells were isolated by FACS from dissociated trunks of 20-24hpf zebrafish and submitted to 10x Sequencing

first: Rytis

last: Prekeris

first: Kristin

last: Artinger


title: RNA Sequencing facilitates quantitative Analysis of differently expressed genes with negative control (NC) and siLINK-A treatment in rheumatoid fibroblast-like synoviocytes [RNA-seq]

summary: To explore how LINK-A regulates the functions of RA FLS,RNA sequencing analysis was used to evaluate the transcriptome of siLINK-A treatment and negative control (NC)  group.P value less than 0.05 was considered significant.

overall_design: Firstly,analyzing differently expressed genes (P<0.05) by RNA sequencing in NC and siLINK-A -treated RA FLSs from three different patients. Secondly, to detect the overlap genes among the three patients.

first: J

first: C

last: Shen

first: R


title: Cyclin D2 overexpression drives B1a-derived MCL-like lymphoma in mice

city: Ghent

first: Wouter

last: Van Loocke

state: East Flanders

address: C. Heymanslaan 10

department: Biomolecular Medicine

country: Belgium

institute: Ghent University

summary: We provide RNA sequencing data for a Ccnd2/p53/Mb1Cre mouse model  (Mb1Cre is active from pre-B cells onwards). This mouse model features Ccnd2 overexpression and p53 loss in B-cells, and develops tumors that resembles Mantle cell lymphoma (MCL). These Ccnd2/p53/Mb1Cre mice develop both non-MCL and MCL-like lymphomas and RNA samples from both groups were sequenced. Fresh lymphoma cells (5x10exp6) were frozen in 700 µl of QIAZOL and stored in -80°C. RNA was prepared using a miRNeasy mini kit (Qiagen).

overall_design: mRNA profiles from non-MCL and MCL-like murine Ccnd2/p53/Mb1Cre lymphomas

first: Pieter

last: Van Vlierberghe

first: Tim

last: Pieters


title: RNA-Seq analysis of gene expression profile of human monocytes infected by Vaccinia Virus

city: Beijing

first: Guoqiang

last: Zhang

address: 1 Beichen West Road, Chaoyang District

institute: INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES

summary: In this study, we employed high throughput sequencing (RNA-Seq) to investigate the gene expression profiles in THP-1 (monocyte cells )before and post-infection of VACV. we conducted RNA-Seq and analyzed differentially expressed genes in THP-1 cells with and without VAVC infection, and then performed the enrichment analysis, function annotation, and STRING network analysis. 4976 genes with significant differential expression (2416 were up-regulated and 2380 were down-regulated). Further KEGG enrichment analysis suggested that 27 significant signaling pathways, including metabolism, immune inflammation regulation, cell function regulation, cancer and myocardial disease, pathogen infection, were affected by VACV infection. Gene Ontology (GO) functional annotation indicated that these genes were mainly enriched on cell level regulation, immunological processes, protein levels, and signal transduction pathway. The STRING online database analysis showed that JUN,CHUK,IL1B,PYCARD protein were higher in the infected THP-1 cells.

overall_design: RNA-seq of Vaccinia virus treatment human monocytes at the indicated stages were generated by deep sequencing, 3 replicates per samplein duplicate, using NovaSeq platform.RIP-seq of human monocytes were generated by deep sequencing, 3 replicates per samplein duplicate, using NovaSeq platform.MeRIP-Seq of human monocytes at the indicated stages were generated by deep sequencing, 3 replicates per samplein, using  illumina Hiseq instrument.

first: Raorao

last: Huo

first: Qinmiao

last: Sun

first: Xiaona


title: Genome-wide ChIP-Seq profiling of a wild-type and a C-terminally truncated mutant of HMR

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Analysis of genome-wide chromatin binding upon overexpression of full length (FL) or C-terminal truncated (dC) HMR in Drosophila SL2 cells

overall_design: Using Drosophila SL2 cells transfected either with full length (FL) or C-terminal truncated (dC) FLAG-HMR, we induced overxpression of the HMR protein and generated genome-wide binding profiles by performing ChIP-Seq with anti-FLAG antibody (n = 5) or with anti-HMR antibody (n=4).

first: Andrea

last: Lukacs

first: Axel

last: Imhof


title: Transcriptome analysis of Clavibacter michiganensis subsp. michiganensis infected tomato seedlings

city: Athens

first: Stamatis

last: Rigas

state: Attiki

address: Iera Odos 75

department: Biotechnology

country: Greece

institute: Agricultural University of Athens

summary: The gram- positive bacterial pathogen Clavibacter michiganensis subsp. michiganensis (Cmm) causes huge economic losses by infecting tomato plants worldwide. Cmm can be spread by contaminated seeds and transplants, penetrating the plant through natural openings or wounds and is transferred through the plant xylem. While in recent years significant progress has been made to elucidate plant responses to pathogenic gram-negative bacteria by gene expression studies, the molecular mechanisms that lead to disease symptoms caused by gram-positive bacteria like Cmm remain elusive. An indigenous virulent Cmm strain isolated from a farm crop of Pomodoro tomatoes in southern Greece was used for the infection of EKSTASIS F1 hybrid tomato seedlings.  Here, we present the results of a deep RNA- sequencing (RNA-seq) analysis performed to characterize the dynamic expression profile of tomato genes upon Cmm infection.

overall_design: Cmm bacteria were grown for 36hrs at 26oC in a rotating shaker, in YPDNM medium containing 1% Yeast extract, 2% Peptone, 2% D-Glucose, 1% NaCl and 10mM MgCl2. Bacteria were pelleted by centrifugation at 1200g for 10 min, washed, and diluted to a titer of 108 cfu/mL in Dilution buffer (10 mM MgCl2, 10mM Tris-HCl pH:6.8). Bacterial suspensions or dilution buffer were injected into the stem region between the cotyledons of 2 week-old plants with a syringe fitted with a 30-gauge needle. For the transcriptome studies, 1 cm sections of the stems above the inoculation site from mock treated and Cmm infected tomato seedlings were collected at 6 and 12 days post inoculation (dpi) for RNA-Seq analysis. Total RNA was extracted using the Direct-zol RNA Miniprep (Zymo research, Irvine CA, USA) kit with an on-column DNase treatment according to the manufacturer’s instructions. The quantity and integrity of RNA were assessed using a NanoDrop ND-1000 spectrophotometer (Thermo Fischer Scientific, Waltham, MA, USA) and agarose gel electrophoresis. RNA-seq libraries were generated using the TruSeq Low Input kit according to the manufacturer’s instructions (Illumina). Sequencing was performed on BGISEQ-500 platform instrument at BGI (Beijing Genomics Institute) in three biological replicates for each sample.

first: Dikran

last: Tsitsekian


title: Biochemistry of spontaneous preterm birth

city: Oulu

first: Antti

last: Haapalainen

address: Aapistie 5A

department: CRC

country: Finland

institute: University of Oulu

summary: Transcriptome analysis of preterm and term placentas

overall_design: RNA-seq analysis of placentas obtained after spontaneous preterm and term births, and after Caesarean section elective term deliveries


title: Global gene expression analysis in NGP CRISPR control cells and NGP ALK(LF655del) cells.

city: Boston

first: Ruben

last: Dries

address: 360 Longwood Ave

department: Computational Biology

institute: DFCI

summary: We performed gene expression profiling by Affymetrix primeview array in both NGP CRISPR control cells and NGP ALK(LF655del) cells.

overall_design: Expression profiles of NGP CRISPR control cells and NGP ALK(LF655del) cells using GeneChip® PrimeView™ Human Gene Expression Array, in triplicate,for a total of 6 individual samples.

first: Hao

last: Huang

first: Rani

last: George


title: Screening of Genes Related to Glucose and Lipid Metabolism in Non-alcoholic Fatty Liver Disease by Gene Microarray

city: Xi’an. China

first: ting

last: li

state: Shaanxi

address: NO.76 Yanta West Road, Health Science Center, Xi’an Jiaotong University, Xi’an. China

department: Health Science Center

institute: Xi’an Jiaotong University

summary: We used gene expression microarray to explore the correlation between gene expression profiles and find out the target genes related to lipid and glucose metabolism in NAFLD. A rat model of NAFLD was established by feeding male rats with high-fat diet and Agilent DNA microarray was used to detect gene expression profiles of liver tissues. We explored differentially expressed genes and intersection of them by using Gene ontology (GO) and Pathway analyses. Then, target genes were verified by Real-time polymerase chain reaction (RT-PCR).   There were 932 genes, including 783 up-regulated and 149 down-regulated, differed  in expression compared to those of control rats. The up-regulated genes were involved in biosynthesis, cell development, cell differentiation and down-regulated genes mainly contributed to biological metabolic process and stress reaction. We identified genes involved in insulin signaling pathway, Notch signaling pathway, adipocytokin and linoleic acid metabolism to be closely related to liver fat content and insulin resistance. Among them, genes which supposed to connect glucose and lipid metabolism were screened  (IGFBP7, Notch1, HMGCR and ACACB) and then validated by real-time PCR. These data provide innovative information on the whole genome expression profile due to high-fat diet feeding and bring important insights into the mechanism of NAFLD.

overall_design: Liver tissues from male rats were distributed into two experimental groups: normal control group (Zheng) and NAFLD tissue group (N), then Agilent DNA microarray was used to detect gene expression profiles of liver tissues

first: Ting

last: Li

first: Xiaolan

last: Lu


title: Effects of REDD1 KO in transcriptomic response to wounding and glucocorticoid treatment in HaCaT human keratinocytes

first: Irina

last: Budunova

address: 303 E. Chicago Ave, WARD 9-015

department: Dermatology

institute: Northwestern University

summary: REDD1 KO affects basal global gene expression profile and transcriptomic response to wounding and glucocorticoid treatment in HaCaT human keratinocytes

overall_design: REDD1 KO HaCaT human keratinocytes were obtained with Crispr/Cas9 technology. The KO and WT (Cas9 only) HaCaT human cells were grown to 90% confluency and treated with either vehicle (WT or KO), 1uM glucocorticoid floocinolone acetonide (FA) (WT_FA or KO_FA), or wounded by scratching (WT_Wound or KO_Wound), or wounded and treated with FA (WT_Wound_FA or KO_Wound_FA), with all conditions incubated for 24 h before harvesting.

first: Gleb

last: Baida


title: Islet Sympathetic Innervation and Islet Neuropathology in Patients with Type 1 Diabetes

status: Public on Aug 09 2021

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

summary: Dysregulation of glucagon secretion in type 1 diabetes (T1D) involves hypersecretion during postprandial states, but insufficient secretion during hypoglycemia. The sympathetic nervous system regulates glucagon secretion. To investigate islet sympathetic innervation in T1D, sympathetic tyrosine hydroxylase (TH) axons were analyzed in control non-diabetic organ donors, non-diabetic islet autoantibody-positive individuals (AAb), and age-matched persons with T1D.  Islet TH axon numbers and density were significantly decreased in AAb compared to T1D with no significant differences observed in exocrine TH axon volume or lengths between groups. TH axons were in close approximation to islet α-cells in T1D individuals with long-standing diabetes. Islet RNA-sequencing and qRT-PCR analyses identified significant alterations in noradrenalin degradation, α-adrenergic signaling, cardiac b-adrenergic signaling, catecholamine biosynthesis, and additional neuropathology pathways. The close approximation of TH axons at islet α-cells supports a model for sympathetic efferent neurons directly regulating glucagon secretion. Sympathetic islet innervation and intrinsic adrenergic signaling pathways could be novel targets for improving glucagon secretion in T1D.

overall_design: Laser microdissected islets from pancreas organ donors were analyzed by RNA-sequencing and bioinformatics to determine differentially regulated genes.

first: Martha

last: Campbell-Thomson

first: Elizabeth

middle: A

last: Butterworth

first: J

middle: L

last: Boatwright

first: Malavika

last: Nair

first: Lith

middle: H

last: Nasif

first: Kamal

first: Andy

middle: Y

last: Revell

first: Clayton

middle: E

last: Mathews

first: Ivan

last: Gerling

first: Desmond

last: Schatz

first: Mark

last: Atkinson


title: The role of cardiomyocyte Muscle Ring Finger-1 (MuRF1) in transcriptional responses to cyclic stretch (Wei HL1 str RNA seq oridata 71917)

city: Indianapolis

first: Monte

middle: S

last: Willis

address: 635 Barnhill Street Drive

institute: University of Indiana School of Medicine

summary: We investigated the role of cardiomyocyte MuRF1 in the transcriptional responses to cyclic stretch (15% biaxial stretch at 1 Hz for 60 min) using the HL-1 cell line.

overall_design: We transiently knocked-down MuRF1 expression in HL-1 cells in 6-well BioFlex® culture plates using Ad.shRNA MuRF1 (or scramble control) transduction for 48 hours (resulting in >50% protein knock-down). Cells were then stretched at 15% uniaxial stretch at 1 Hz for 60 min in a computer-regulated Flexcell® FX-5000™ Compression System (Flexcell International Corporation, Hillsborough, NC), with parallel non-stretched cells (0 min stretch) used as a control.

first: Wei

last: Tang


title: Next generation sequencing following CUX1 knockdown in erythroblasts

first: Stephanie

middle: N

last: Konecki

address: 625 W Madison, Apt 1904

institute: The University of Chicago

summary: Anemia is a significant cause of morbidity and mortality in myeloid malignances. Cytogenetic changes are recurrent within malignant hematopoietic stem and progenitor cells, yet their role in anemia pathogenesis remains unknown. One recurrent karyotypic abnormality in myeloid neoplasms is the deletion of part or all of chromosome 7 [-7/del(7q)], which harbors the transcription factor and tumor suppressor gene, CUX1. CUX1 knockdown mouse models develop myeloid disease similar to that seen in humans, including a spontaneous, cell intrinsic, and lethal anemia that develops with age. Here, we elucidate the cellular and molecular mechanisms by which CUX1 regulates erythropoiesis. We demonstrate CUX1 knockdown mice have an aberrant stress erythropoiesis response and decreased survival after acute anemia induction. CUX1 insufficient erythroblasts undergo accelerated cell cycling and increased apoptosis. In line with these phenotypes, transcriptome profiling indicates that CUX1-knockdown elicits increased proliferation and decreased erythroid differentiation gene signatures. ATAC-sequencing demonstrated dramatic, global chromatin opening in CUX1-knockdown erythroblasts. As measured by fluorescence lifetime imaging, this increased chromatin accessibility is concomitant with a disruption in nuclear condensation, which is normally requisite in mammalian erythroblasts for nuclear eviction and terminal differentiation. Finally, we show that CUX1 mediates chromatin compaction by promoting histone deacetylation. Thus, rather than a transcriptional role, our data implicate in an epigenetic regulatory role for CUX1 in erythropoiesis. Furthermore, these results suggest therapeutic targeting of epigenetic regulators, such as histone acetyl transferases, may have clinical benefit for the anemias associated with loss of CUX1.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-seq and ATAC-seq following CUX1 knockdown in Megakaryocyte erythrocyte progenitors and RII-basophilic erythroblasts. CUT&RUN for CUX1 in human CD34 erythroblasts. ChIP-seq for CUX1 in K562 cell line

first: Dhivyaa

last: Anandan

first: Jeffrey

last: Kurkewich

first: Megan

last: McNerney


title: Signaling Response to Early Oncogenesis by a Novel Panel of Murine Mutant Kras Alleles in the Mouse Lung Transcriptome [II]

city: Durham

first: Ozgun

last: Erdogan

state: NC

address: 308 Research Dr.

department: Pharmacology and Cancer Biology

institute: Duke University

summary: Despite over 50 oncogenic RAS mutations, specific mutations track with distinct cancer types.  To elucidate the underlying contribution of oncogenic signaling to RAS mutation patterns we globally activated a novel panel of endogenous murine Kras alleles with biochemically distinct mutations encoded with native or common codons producing low or high protein levels.  Each induced unique tumor patterns, with quantitative signaling favoring hematopoietic tumors, qualitative signaling favoring squamous tumors, while carcinomas tended to be a combination of both types of signaling.  Mechanistically, these mutants generated very different levels of active Kras and cellular responses, with low Kras activity yielding transcriptional features of a multipotent state while high activity had all the hallmarks of potent oncogenic activity and resultant stress and an inflammatory response.  We thus suggest that the RAS mutational bias to specific cancer types is a result of tissue-specific responses of normal cells to either or both quantitative and qualitative signaling differences imparted by the selected mutant.

overall_design: Lung transcriptome of three male and female adult mice from KrasnatG12D, KrasnatQ61R, KrascomG12D, KrascomQ61R, and wildtype Kras allele in the Rosa26Cre-ERT2 background 1 week after tamoxifen injection

first: Christopher

last: Counter


title: RNA-sequencing reveals niche gene expression effects of beta-hydroxybutyrate in primary myotubes

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Various forms of fasting, including time-restricted feeding, alternate day fasting, and periodic fasting have shown promise in clinical and pre-clinical studies to normalize body weight, improve metabolic health, and protect against disease. Recent studies suggest that β-hydroxybutyrate (βOHB), a characteristic ketone body of the fasted metabolic state, acts as a potential signaling molecule mediating the beneficial effects of the various forms of fasting, potentially by acting as a histone deacetylase inhibitor. In the first part we investigated whether βOHB, in comparison to the well-established histone deacetylase inhibitor butyrate, influences cellular differentiation in vitro. In C2C12 myotubes, 3T3-L1 adipocytes, and THP-1 monocytes, millimolar concentrations of βOHB did not alter differentiation, as determined by gene expression and histological assessment, whereas equimolar concentrations of butyrate potently impaired differentiation in all cell types. RNA-sequencing revealed that unlike butyrate, βOHB minimally impacted gene expression in adipocytes, macrophages, and hepatocytes. However, in myocytes, βOHB upregulated genes involved in the TCA cycle and oxidative phosphorylation, while downregulating genes belonging to cytokine and chemokine signal transduction. Overall, our data do not support the notion that βOHB serves as a powerful signaling molecule regulating gene expression in adipocytes, macrophages and hepatocytes, but suggest that βOHB may act as a niche signaling molecule in muscle.

overall_design: Mouse primary cells (adipocytes, macrophages, skeletal myotubes, hepatocytes) were exposed to β-hydroxybutyric acid (bOHB; 5mM), butyric acid (5mM), or control treatment, and subjected to gene expression profiling by RNA-sequencing.

first: Philip

last: Ruppert

first: Lei

last: Deng

middle: J

first: Roland

middle: W

last: Hangelbroek

first: Anja

last: Zeigerer

first: Sander

last: Kersten


title: Signaling Response to Early Oncogenesis by a Novel Panel of Murine Mutant Kras Alleles in the Mouse Lung Transcriptome [I]

overall_design: Lung transcriptome of three male and female adult mice from KrasnatG12D, and KrascomQ61R allele in the Rosa26Cre-ERT2 background 1 week after tamoxifen injection


title: IRS1 phosphorylation underlies the non-stochastic probability of cancer cells to persist during EGFR inhibition therapy [Exp1]

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

summary: We found that differential serine/threonine phosphorylation of the insulin receptor substrate 1 (IRS1) protein determines the chance to persist (CTP) of lung and of head and neck cancer cells under EGFR inhibition, both in vitro and in vivo.

overall_design: comparing between naïve untreated cells and Gefitinib treated cells

first: Ravid

last: Straussman

first: Adi

last: Berger


title: RNA Sequencing facilitates quantitative analysis of lncRNA and mRNA expression in fibroblast-like synoviocytes from rheumatoid arthritis patients and trauma patients [microarray]

first: Jingnan

last: Wang

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Fibroblast-like synoviocytes (FLS), the active resident cell component in synovial intimal lining, play a critical role in aggressive action of synovial pannus tissue. The underlying mechanism of FLSs  in the progression of RA is still unknown. To evaluate the expression pattern of lncRNA and mRNA, we preformed microarray to determine its expression profiles in FLS separated from RA patients and trauma patients.

overall_design: FLSs were seperated from synovial tissues and cutured until passage 4. Total RNA was prepared using TRIzol from HC FLS (n=5) and RA FLS (n=5) and quantified by NanoDrop ND-1000.

first: J

first: C

last: Shen

first: R

last: Li


title: IRS1 phosphorylation underlies the non-stochastic probability of cancer cells to persist during EGFR inhibition therapy [Exp3]

overall_design: RNA-Seq of different PC9 single-cell-derived clones with known CTP under gefitinib  (low, intermediate,high)


title: IRS1 phosphorylation underlies the non-stochastic probability of cancer cells to persist during EGFR inhibition therapy.

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: IRS1 phosphorylation underlies the non-stochastic probability of cancer cells to persist during EGFR inhibition therapy [Exp2]

overall_design: comparing between naïve untreated PC9 cells and PC9 cells that were released from gefitinib treatement


title: Cardiotrophin Like Cytokine Factor 1 (CLCF1) alleviates bone loss and osteoclastogenesis in osteoporosis mouse models through activating interferon signaling and repressing the nuclear factor-κB signaling pathway

city: Sapporo

first: Mohamad Alaa

last: Terkawi

state: Hokkaido

address: Kita-15, Nish-7, Kita-ku

department: Department of Orthopedic Surgery

country: Japan

institute: Hokkaido University

summary: We explored the functional role of CLCF1 in osteoclastogenesis and bone loss associated with osteoporosis. Surprisingly, the administration of recombinant CLCF1 repressed excessive bone loss in ovariectomized mice and reduced the levels of local osteolytic lesions induced by a RANKL injection. Likewise, the addition of recombinant CLCF1 to RANKL-stimulated monocytes resulted in a significant suppression in the number of differentiated osteoclasts and their resorption activity on dentine slices.

overall_design: RNA-seq for macrophages stimulated by macrophage colony-stimulating factor, receptor activator of nuclear factor kappa-b ligand and CLCF1

first: Matsumae

last: Gen

first: Shunichi

last: Yokota

first: Terkawi

last: Alaa

first: Iwasaki

last: Norimasa


title: RNA sequencing of flow sorted Scgb1a1 lineage traced Control and Yap/Taz knockout lung epithelial cells

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: Proper lung function relies on precisely balanced numbers of specialized epithelial cell types that work together and are maintained in homeostasis. In this study we have described essential roles for the transcriptional regulators YAP and TAZ, which are key effectors of Hippo pathway signaling, in maintaining lung epithelial homeostasis. Phenotypes associated with Yap/Taz deletion include alveolar defects and a striking development of goblet cell metaplasia throughout the airways. Lineage specific deletion of Yap and Taz in Scgb1a1+ cells leads to increased Mucin production within the knockout cells in vivo. In order better characterize the in vivo transcriptional changes associated with Yap/Taz knockout in these cells, we have isolated Scgb1a1 lineage traced cells from control and yap/taz cNull mice and performed bulk RNA sequencing.

overall_design: Control and Yap/Taz cNull Scgb1a1CreER mice were administered ip tamoxifen for 5 consecutive days at approximately 8 weeks of age. Samples were analyzed 12 days from onset on tamoxifen administration. Lineage traced cells were isolated by FACS from collagenase-dissociated lung tissue and total RNA was isolated for sequencing.

first: Julia

last: Hicks-Berthet

first: Xaralabos

last: Varelas


title: Relative gene expression of the lateral choroid plexus isolated from Abhd2+/+ and Abhd2-/- mice

city: Berkeley

first: Ida

last: Björkgren

state: CA

address: 221A Weill Hall UC Berkeley

department: Department of Molecular and Cell Biology

institute: University of California, Berkeley

summary: Electrophysiological studies of mouse choroid plexus show potentiation of the Kir7.1 channel by progesterone (P4). The choroid plexus (CP) epithelium contains several membrane-bound progesterone receptors that could potentially mediate the cell response to P4. Interestingly, we found that the recently characterized progesterone receptor α/β hydrolase domain–containing protein 2 (ABHD2)(Miller et al., 2016) is also highly expressed in the CP. ABHD2 has been shown to regulate ion channel activation in human sperm cells by breaking down the endocannabinoid 2-arachidonoylglycerol in the cell membrane(Miller et al., 2016). However, CPECs isolated from global Abhd2 knockout mice that were generated in our lab(Ida Björkgren, 2019) showed similar expression and activation of Kir7.1 as cells from wild type animals, thus negating any possible effect of the receptor on Kir7.1 activation.

overall_design: For gene expression analyses of the mouse choroid plexus, the lateral chroid plexuses (LCPs) of adult Abhd2+/+ (wt) males (n=3) and females (n=3) and of Abhd2-/- (hoz) males (n=3) and females (n=3) were used.

first: Sarah

last: Mendoza

first: DongHwa

last: Chung

first: Monika

last: Haoui

first: Natalie

last: Petersen

first: John

last: DellaRosa

first: Polina

middle: V

last: Lishko


title: A composite DNA element that functions as a maintainer required for epigenetic inheritance of heterochromatin

first: Xiaoyi

last: Wang

address: 240 Brookline Ave

institute: Harvard Medical School

summary: Epigenetic inheritance of heterochromatin requires sequence - independent propagation mechanisms and input from DNA sequence, but how DNA contributes to inheritance is not understood. Here, we identify a DNA element ( term ed the “maintainer” ) that is necessary and sufficient for epigenetic inheritance of preexisting histone H3 lysine 9 methylation (H3K9me) and heterochromatin i n the fission yeast Schizosaccharomyces pombe . In wild - type cells, d espite its requirement for maintenance of H3K9me, the maintainer cannot establish de novo gene silencing. The maintainer is a composite 1307 - base pair DNA element with binding sites for the Atf1/Pcr1 and Deb1 transcription factors and the O rigin R ecognition C omplex (ORC) and can be converted to a silencer in cells with lower rates of H3K9me turnover , suggesting that it participate s in recruiting the H3K9 methyltransferase Clr4 / Suv39h . T hese results suggest tha t histone H3K9me is only heritable when it can collaborate with maintainer - associated DNA - binding proteins that help recruit the enzyme responsible for its epigenetic deposition .

overall_design: Examination of genomic localization of Atf1/Pcr1, Deb1 and ORC in S.pombe

first: Danesh

last: Moazed


title: Functional convergence of growth responses to shade and warmth in Arabidopsis

city: CABA

first: Carlos

middle: Esteban

last: Hernando

state: Buenos Aires

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundacion Instituto Leloir

summary: The goal of this study was to compare the transcriptional profile (RNA-seq) of Arabidopsis thaliana Columbia-0 ecotype seedlings that were treated with two different light (white light or shade) and temperature (20ºC or 28ºC) conditions.

overall_design: Seeds of Arabidopsis thaliana were sown on 0.8 % agar-water in Petri dishes, stratified 5-7 d at 5 ºC in darkness and transferred to a growth room at 22°C with a photoperiod of 10 h of 100 μmolm −2 s −1 of white light (400–700 nm) provided by a mixture of fluorescent and halogen lamps (red/far-red ratio = 1.1). Three-day-old seedlings of the wild type Columbia were exposed during the photoperiod of day 4 (10 h) to white light at 20°C, white light at 28°C, shade at 20°C or shade at 28°C. Three biological replicates of each condition were collected at the end of the photoperiod of the day 4.

first: J

last: Casal

first: S

middle: G

last: Romero-Montepaone

first: C


title: USP19 and RPL23 as candidate prognostic markers in advanced-stage high-grade serous ovarian carcinoma

city: Sengnam

first: Sohyun

last: Hwang

address: 59, Yatap-ro, Bundang-gu

department: Pathology

country: South Korea

institute: Cha University

summary: Ovarian cancer is one of the leading causes of death among patients with gynecological malignancies worldwide. To identify prognostic markers for ovarian cancer, we performed RNA-sequencing and analyzed the transcriptome data from 51 patients who received conventional therapies for high-grade serous ovarian carcinoma (HGSC). Patients with early-stage (I or II) HGSC exhibited higher immune gene expression than patients with advanced stage (III or IV) HGSC. To predict the prognosis of HGSC patients, we created machine learning-based models and identified RPL23 and USP19 as candidate prognostic markers. Specifically, patients with higher RPL23 mRNA levels had a worse prognosis and patients with higher USP19 mRNA levels had a better prognosis. This model was then used to analyze HGSC patient data hosted on The Cancer Genome Atlas; this exercise validated the prognostic abilities of these two genes with respect to patient survival. Taken together, the transcriptome profiles of RPL23 and USP19 determined using a machine-learning model could serve as prognostic markers in HGSC patients receiving conventional therapy.

overall_design: The mRNA expression of 51 primary high-grade serous ovarian cancer were measured by RNA sequencing.

first: Hee

last: An


title: Global transcriptomic changes in human lung fibroblasts MRC5 exposed to conditioned media from RAS-activated alveolar epithelial type II (ATII) cells based on RNA-seq.

city: Southampton

first: Yihua

address: University Road

country: United Kingdom

institute: University of Southampton

summary: IPF (idiopathic pulmonary fibrosis), a progressive lung disease with an unmet need for treatment, causes increased morbidity and mortality worldwide. Abnormal wound healing is strongly implicated in IPF, but the underlying mechanisms remain poorly understood. Here we reported that aberrant epithelial-mesenchymal crosstalk provides self-sustaining pro-fibrotic signals in IPF. By performing RNA-sequencing (RNA-seq) in human lung fibroblasts MRC5 treated with either conditioned media (CM) from control or 4-OHT (4-hydroxytamoxifen) - treated ATIIER:KRASV12 cells (kindly provided by Prof Julian Downward, The Francis Crick Institute, UK), in which addition of 4-OHT acutely activates RAS pathway (Yao et al. Cell Death & Differentiation 2019), we identify several IPF-related pathological alterations. These include increases in GO terms related to extracellular matrix (ECM) and collagen, cell migration, and inflammatory response. Our data suggest that RAS-activated ATII cells crosstalk to MRC5 lung fibroblasts to augment their activation and migration.

overall_design: To assess the global transcriptomic changes in lung fibroblasts exposed to conditioned media from RAS-activated ATII cells. In the control group (control), MRC5 lung fibroblasts were dosed with conditioned media collected from control ATIIER:KRASV12 cells for 24 hours. In the 4-OHT group (4-OHT), MRC5 lung fibroblasts were dosed with conditioned media collected from 4-OHT-treated ATIIER:KRASV12 cells for 24 hours. RAS activation was induced by addition of 4-OHT to ATIIER:KRASV12 cells for 24 hours, and conditioned media were then collected. After treatment, MRC5 cells were subjected to RNA-seq (n=3 for each group).

first: L

last: Yao

first: Y

last: Zhou


title: Yap/Taz inhibit goblet cell fate to maintain lung epithelial homeostasis

first: Boston University

last: Microarray and Sequencing Resource

summary: Proper lung function relies on precisely balanced numbers of specialized epithelial cell types that work together and are maintained in homeostasis. We describe essential roles for the transcriptional regulators Yap and Taz, which are key effectors of Hippo pathway signaling, in maintaining lung epithelial homeostasis. We report that conditional deletion of Yap1/Yap and Wwtr1/Taz in the lung epithelium of adult mice results in severe defects with consequent animal lethality. Phenotypes associated with Yap/Taz deletion include alveolar defects and a striking development of goblet cell metaplasia throughout the airways. We performed gene expression analysis of wild type and Yap/Taz null primary mouse airway epithelial cells in order to define Yap/Taz controlled gene expression.

overall_design: Primary mouse airway epithelial cells were isolated from the tracheas of YapF/F; TazF/F; RosaCreER and YapF/F; TazF/F; No Cre mice. Cells were grown to confluence on collagen coated transwells in triplicate for each condition. All cells were cultured in the presence of 3uM 4-hydroxytamoxifen for 5 days in submerged mouse ALI expansion medium.  RNA was extracted using the RNeasy Kit (Qiagen), subjected to Bioanalyzer quality assessment, and analyzed by Affymetrix Mouse Gene 2.0 ST array.

first: Julia

last: Berthet

first: Xaralabos

last: Varelas


title: Single-cell deciphering of human fetal innate  lymphoid cell development

first: Gong

last: Yandong

address: DongDaJie #8

institute: the Fifth Medical Center of the PLA General Hospital

summary: The functions of innate lymphoid cells (ILCs) in immune system are increasingly appreciated, whereas the early development of ILCs in human remains elusive. In this study, we sorted humanhematopoietic stem progenitor cells, lymphoid progenitors, presumed ILC progenitor/precursors and mature ILCs in the fetal hematopoietic, lymphoid and non-lymphoid tissues, from 8 to 12 PCW,for single-cell RNA-sequencing, followed by computational analysis and functional validation. We  delineated the early phase of ILC development, from hematopoietic stem progenitor cells to multipotent lymphoid progenitors and to ILC progenitors, which mainly occurred in fetal liver and intestine. We further unveiled interleukin-3 receptor alpha (IL-3RA) as the surface marker for the lymphoid progenitors with T cell, B cell and ILC potentials. Notably, we determined the heterogeneity and tissue distribution of each ILC subpopulation, revealing the shared proliferating characteristics of the precursors of each ILC subtype. Additionally, a novel unconventional ILC2 subpopulation (CRTH2-CCR9+ ILC2) was identified in fetal thymus. Taken together, our study illuminates the precise cellular and molecular features underlying the stepwise formation of human fetal ILC hierarchy with remarkable spatiotemporal heterogeneity.

overall_design: Here, we provided an unprecedented single-cell transcriptome atlas of stepwise ILC ontogeny in early human fetus using cells from fetal hematopoietic, lymphoid and non-lymphoid tissues spanning 8 to 12 post-conception weeks (PCWs).

first: Chen

last: Liu

first: Yandong

last: Gong


title: Single-cell RNA sequencing of niche cells from WT, BMT and aGVHD mice

city: Tianjin

first: Quan

last: Gu

address: 288 Nanjing Road

institute: State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital

summary: We performed scRNA-seq of non-hematopoietic cells from non-treated control (WT), BMT and aGVHD mice. Unsupervised clustering, sub-clustering based on gene expression and trajectory analysis converged on the conclusion that aGVHD likely disrupts MSC differentiation potential, especially osteogenesis.

overall_design: Examination of gene expression profiles in WT, BMT and aGVHD sample

first: Yan

last: Lin

first: Hui

last: Cheng

first: Tao


title: Comparative analysis of brain transcriptomes altered during JEV infection in wild type and IRF8 knockout C57Bl/6 mice

city: Faridabad

first: Arup

last: Banerjee

state: Haryana

address: NCR Biotech Science Cluster

country: India

institute: Regional Centre for Biotechnology

summary: Japanese encephalitis virus (JEV) is a causative agent of encephalitis, mostly prevalent in Asia and South-Asian countries. Neuroinflammation is the hallmark of encephalitis, mediated in parts through the activation of brain-resident microglial cell, thus playing a critical role in determining pathogenesis. Deregulated activity of microglia can be lethal for the brain tissue. Interferon Regulatory Factor 8 (Irf8) mediates differentiation and transformation of microglia to reactive phenotypes and also regulates antiviral response through cross-talk with interferon pathway.  In this study, we have conducted a comparative study between JEV infected C57BL/6 wild type and Irf8 Knockout (IRF8-/-) to identify the genes directly or indirectly regulated by IRF8.

overall_design: In this study,we included 4 group- C57BL/6 wild type-mock (n=2) ,WT_JEV (n=3), IRF8-/- mock (n=2), IRF8-/-_JEV (n=3)

first: Aarti

last: Tripathy

first: Bhupender

last: Singh

first: Praful

middle: K

last: Tailor


title: Next Generation Sequencing Quantitative Analysis on COVID-19 Kidney tissue

city: New York

first: Weijia

last: Zhang

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

summary:
Purpose: The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of COVID-19 kidney to normal controls
Methods/Results: Kidney mRNA profile of human COVID-19 tissue was generated by deep sequencing using Illumina Novaseq6000 Paired-end 150.  After filtering reads mapped to contamination database, the reads that were uniquely aligned to the exon and splicing-junction segments with a maximal 2 mismatches for each transcript were then counted as expression level for corresponding transcript. Next, RNA-seq reads count data were downloaded from public resource GTEx project (https://www.gtexportal.org/home/datasets) and 12 normal kidney tissue samples were extracted as controls. The differential analysis by fold change difference was carried out to identify dysregulated genes at 1.5 fold change. The differential expressed genes were then subjected to Gene Ontology function and Pathway (KEGG, Ingenuity IPA, BIOCARTA, NABA, Panther, PID, REACTOME, Wiki-pathway) enrichment analysis by Fisher-exact test.
Conclusions: RNA sequencing data revealed that biological processes from upregulated genes were enriched for cell cycle, chromosome segregation, response to wounding, humoral immune response, and blood coagulation, suggesting that cell injury/regeneration, inflammatory response, and endothelial injury were the major disease processes involved. The biological processes from downregulated genes were enriched for ion transport, metabolic processes, and oxidation, likely secondary to severe tubular cell injury. Pathway analysis from both up- and downregulated genes showed enrichment of transmembrane transport, oxidation, and blood coagulation consistent with the GO terms analysis. Upregulated genes were enriched only for the FOXM1 pathway, which was recently reported to promote tubular cell proliferation during injury repair. Additionally, genes related to the renin-angiotensin system were downregulated, but ACE2 expression did not differ from normal controls.

first: Jia

last: Fu

first: Zhengzi

last: Yi

first: John

last: He

first: Kirk

last: Campbell


title: Combined analysis of transcriptome and metabolome to molecular mechanism research of source–sink modifications

city: Jinan

first: Huawei

last: Li

address: North Industry Road

institute: Crop Research Institute, Shandong Academy of Agricultural Sciences

summary: we use metabolomics to explore the changes of metabolites after the Source–Sink modifications, and combined with transcriptomics to explore its molecular mechanism at the genetic level

overall_design: A total of 18 transcriptome samples under different treatments


title: single-cell RNA sequencing  reveals the mechanism of human breast cancer metastasis

status: Public on Aug 08 2021

city: Nanjing

first: kun

last: xu

address: guangzhou road 300

institute: Department of Oncology, The First Affiliated Hospital of Nanjing Medical University

summary: To obtain more information about the lymph node metastasis of breast cancer cells, we selected the matched primary breast cancer (PC), positive lymph nodes (PL), and negative lymph nodes (NL) of the same patient to perform integrated analysis. The PC, PL, NL samples were analysed with single-cell RNA sequencing.

overall_design: The matched primary breast cancer (PC), positive lymph nodes (PL), and negative lymph nodes (NL) samples were analysed with single-cell RNA sequencing.

first: Kun

last: Xu


title: single-cell ATAC sequencing reveals the mechanism of human breast cancer metastasis

summary: To obtain more information about the lymph node metastasis of breast cancer cells, we selected the matched positive lymph nodes (PL), and negative lymph nodes (NL) of the same patient to perform integrated analysis. The PL, NL samples were analysed with single-cell ATAC sequencing.

overall_design: Single cell ATACseq was performed using the 10X Genomics platform per the manufacturers instructions.


title: Real-time quantitative PCR analysis of baboon cerebellum oligodendrocytes

city: San Antonio

first: Elizabeth

last: Gould

state: Texas

address: 7703 Floyd Curl Dr

institute: University of Texas Health Science Center San Antonio

summary: Oligodendrocytes were aspirated after electrophysiology recordings for qPCR analysis from cerebellum slices

sample_organism:
Papio anubis
Mus musculus
synthetic construct

overall_design: qPCR gene expression profiling.

first: Jun

last: Kim


title: Gene Expression Profile Analysis of Gallic Acid-induced Cell Death Process

city: Shatin

first: Ho Man Holly

last: Tang

address: Science Centre South Block

department: School of Life Sciences

institute: The Chinese University of Hong Kong

summary: Gallic acid is a natural phenolic compound that displays anti-cancer properties in clinically relevant cell culture and rodent models. To date, the molecular mechanism governing the gallic acid-induced cancer cell death process is largely unclear, thus hindering development of novel therapeutics. Therefore, we performed time-course long non-coding RNA sequencing (lncRNA-seq) to reveal the gene expression profiles at the early, middle, and late stages of the gallic acid-induced cell death process in human cervical cancer HeLa cells. This work provides a dataset with differentially expressed genes across different stages of cell death process during the gallic acid induction, which is important for further study on the control of this cell death mechanism.

overall_design: There are 15 samples in total (5-time points x 3 replicates). Time points include: HeLa cells treated with gallic acid (50 µg/mL) for 0 hour (GA0hr), 2 hours (GA2hr), 4 hours (GA4hr), 6 hours (GA6hr), and 9 hours (GA9hr).

first: Ho

middle: M

first: Chi

last: Cheung


title: Real-time quantitative PCR analysis of mouse cerebellum oligodendrocytes

sample_organism:
Homo sapiens
Mus musculus
synthetic construct


title: Quantitative analysis of ERR gamma conditional knock-out (cKO) acinar cell transcriptome

city: Daejeon

first: Jinhyuk

last: Choi

address: 291, Daehak-ro, Yuseong-gu

institute: KAIST

summary: The goal of this study is to compare NGS-derived pancreatic acinar cell transcriptome profiling (RNA-seq) to analyze the alteration of transcriptional program depending on ERR gamma expression.

overall_design: Gene expression profiling on ERR gamma conditional knock-out in pancreatic acinar cells.

first: Jae

last: Suh


title: Genome-wide assessment of GSK-J4-treated lung adenocarcinoma cell lines

city: DaeJeon

first: Mi Young

address: Biological science

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Genome-wide RNA-seq from GSK-J4-treated lung adenocarcinoma cell lines

summary:
Purpose: The goals of our study were to identify downstream pathway regulated by GSK-J4 in lung adenocarcinoma
Methods: RNAs isolated from GSK-J4-treated or untreated lung adenocarcinoma (HCC827, H23 and A549) were analyzed by using an Illumina Nextseq500
Conclusions: Our study represents the first detailed transcriptomic analysis of effects of GSK-J4 in lung adenocarcinoma.

overall_design: mRNAs prepared from GSK-J4-treated or untreated lung adenocarcinoma cell lines were analyzed in duplicaters by Illumina Nextseq500.

first: Beom-jin

last: Hong

first: Mi

first: Jae-Seok

last: Roe


title: Real-time quantitative PCR analysis of mouse brainstem oligodendrocytes, mouse cerebellum oligodendrocytes and baboon cerebellum oligodendrocytes

sample_organism:
Papio anubis
Homo sapiens
Mus musculus
synthetic construct

platform_organism:
Papio anubis
Mus musculus


title: micro-like RNAs and their targets engage in DCL2-deleted Valsa mali

status: Public on Aug 07 2021

city: Yangling

first: Ming

address: No. 3, Taicheng Road

department: College of Plant Protection

institute: Northwest A&F University

summary: Dicer proteins are mainly responsible for generating small RNAs (sRNAs). In previous study, two DCL proteins in Valsa mali, the pathogenic fungus of apple tree Valsa canker, were found to be associated with the pathogenicity and generation of sRNAs. In this study, we constructed two milRNA libraries using the the wild-type 03-8 (MVm) and Vm-DCL2 deletion mutant (MD2) strains and the differential expression of miRNA-like RNAs (milRNAs) were analyzed based on the deep-sequencing of the wild-type and Vm-DCL2 mutant, respectively. In total, by comparing the expression difference of milRNAs between MVm and MD2, it was found that 33 milRNAs were not detected in MD2, 28 milRNAs were both detected in MVm and MD2. By statistical analysis, one and 17 milRNAs showed up-regulated and down-regulated expression in MD2 compared with MVm, respectively (p<0.05). Importantly, 10 milRNAs were not detected in MD2, and identified to be DCL2 dependent milRNAs. We also identified the target genes of these milRNAs using degradome sequencing technology and found they were associated with protein phosphatase, isocitrate dehydrogenase, phosphoglycerate mutase, etc. The study will lay a foundation for the comprehensive analysis of pathogenic mechanisms of V. mali, and enrich cognition of the generation and function of fungal sRNA.

overall_design: milRNAs were isolated using high-throughput sequence analysis and their corresponding target genes were identified using degradome sequencing technology.

first: Feiran

last: Guo

first: Jiahao

last: Liang

first: Gao

first: Lili

last: Huang

first: Hao

last: Feng


title: Next Generation Sequencing Based RNAseq Analysis of lri25-/- mutant zebrafish larvae at 5 dpf.

city: Cleveland

first: Takuya

last: Sakaguchi

address: 9500 Euclid Ave.

institute: Cleveland Clinic Foundation

summary: Gene expression profiles in lri25 mutant zebrafish larvae at 5 dpf based on the RNAseq data.

overall_design: Total RNA was isolated from homozygous lri25 mutant and their clutchmate wild-type larvae at 5 dpf.  Gene expression difference between wild-type and lri25 mutant larvae was determined based on the RNAseq data.


title: CytoScan 750K array data for the ataxia patient's sample

city: Yongin-si

first: Chang Ahn

last: Seol

state: Gyeonggi-do

address: 107, Ihyeon-ro 30beon-gil, Giheung-gu

department: Genome Research Center

institute: GC Genome

type:
Genome variation profiling by array
Genome variation profiling by SNP array

summary:
CytoScan 750K array was performed for the detection of CNV associated with the patient's phenotype
CytoScan 750K array was performed according to the manufacturer's directions on DNA extracted from peripheral blood sample.

overall_design: Copy number analysis of CytoScan 750K array was performed for the patient's sample (case report)

first: Chang

last: Ki

first: Dae

last: Jang


title: Genome-wide ChIP-Seq from GSK-J4 or siKDM6B-treated lung adenocarcinoma cell line A549

summary:
Purpose: The goals of our study were to identify downstream pathway regulated by GSK-J4 in lung adenocarcinoma
Methods: Chromatin isolated from GSK-J4- or siKDM6B-treated lung adenocarcinoma with proper controls was used to generate ChIP-Seq libraries

overall_design: ChIP-Seq with indicated antibodies (H3K27me3 or H3K4me3) of human lung adenocarcinoma cell lines with various conditions


title: Associations of immune cell homing gene signatures and infiltrates of lymphocyte subsets in human melanomas: discordance with CD163+ myeloid cell infiltrates

city: Tucson

first: Dominic

last: LaRoche

state: AZ

address: 3430 E. Global Loop

institute: HTG Molecular Diagnostics

summary:
Background: Immune cells in the tumor microenvironment have prognostic value.  In preclinical models, recruitment and infiltration of these cells depends on immune cell homing (ICH) genes such as chemokines, cell adhesion molecules, and integrins.  We hypothesized ICH ligands CXCL9-11 and CCL2-5 would be associated with intratumoral T-cells, while CXCL13 would be more associated with B-cell infiltrates.
Methods: Samples of human melanoma were submitted for gene expression analysis and immune cells identified by immunohistochemistry.  Associations between the two were evaluated with unsupervised hierarchical clustering using correlation matrices from Spearman rank tests.  Univariate analysis performed Mann-Whitney tests.
Results: For 119 melanoma specimens, analysis of 78 ICH genes revealed association among genes with nonspecific increase of multiple immune cell subsets: CD45+, CD8+ and CD4+ T-cells, CD20+ B-cells, CD138+ plasma cells, and CD56+ NK-cells.  ICH genes most associated with these infiltrates included ITGB2, ITGAL, CCL19, CXCL13, plus receptor/ligand pairs CXCL9 and CXCL10 with CXCR3; CCL4 and CCL5 with CCR5.  This top ICH gene expression signature was also associated with genes representing immune-activation and effector function. In contrast, CD163+ M2-macrophages was weakly associated with a different ICH gene signature.
Conclusion: These data do not support our hypothesis that each immune cell subset is uniquely associated with specific ICH genes. Instead, a larger set of ICH genes identifies melanomas with concordant infiltration of B-cell and T-cell lineages, while CD163+ M2-macrophage infiltration suggesting alternate mechanisms for their recruitment.  Future studies should explore the extent ICH gene signature contributes to tertiary lymphoid structures or cross-talk between homing pathways.

overall_design: Relative expression of homing molecule mRNA was assessed on FFPE samples using the HTG EdgeSeq Oncology Biomarker Panel and compared with IHC-identified immmune cells on the same melanoma samples.

first: Craig

last: Slingluff Jr.

first: Minyoung

last: Kwak


title: RNA-Seq of SARS-Cov-2 Infection in Human Airway Epithelium Organoids

city: Shenzhen

first: Liang

last: Yang

address: No. 1088 Xueyuan Avenue, Nanshan District

institute: SUStech

summary: We performed RNA-Seq of SARS-Cov-2 infection in human airway epithelium organoids. The organoids were infected with SARS-Cov-2 for 24hours or 48hours respectively, and compared with uninfected mock control.

overall_design: The airway epithelium organoids were infected with SARS-Cov-2 for 24hours or 48hours respectively, and compared with uninfected mock control.

last: Li


title: Next Generation Sequencing (m6A-seq) Reveals RNA m6A Methylation Patterns During the floral transition of Arobidopsis

city: Xuzhou

first: Tao

last: Xu

state: Jiangsu

address: Shanghai Road 101

institute: Jiangsu Normal University

summary: In this study, we identified METTL16 as an mRNA m6A methyltransferase that plays a vital role in the floral transition in Arabidopsis. Transcriptome-wide analysis of RNA methylome in the mettl16 mutant revealed that m6A modification enriched near the stop codon and within the 3ʹ untranslated region. Deficiency of METTL16 leads to decreases in m6A levels of approximately 471 transcripts, indicating that it is responsible for the methylation of a small group of mRNAs. The mettl16 mutant displayed an early flowering phenotype, and the level of FLOWERING LOCUS C (FLC) was markedly decreased in the mutant. Importantly, METTL16-mediated m6A methylation affects the splicing of FLC, thereby influencing its transcript level to regulate floral transition. Our study identified METTL16 as a novel m6A methyltransferase and suggests a close molecular link between METTL16-mediated m6A methylation and FLC splicing in flowering time control.

overall_design: The Arobidopsis Col-0 and mettl16 mutant seedling were collected at 3-week-old. And the RNA extracted from samples with three biological replicates was subjected to m6A and RNA sequencing. For data analysis, the 3-week-old seedling of Col-0 was used as reference sample to investigate the role of m6A in floral transition.

first: Hunseung

last: Kang


title: RNA-Immunoprecipitation Sequencing of Actinin-BirA* vs. Control iPSC-CMs

city: Farmington

first: Travis

last: Hinson

state: Connecticut

address: 10 Discovery Dr

institute: JAX-GM

summary: We found an enrichment of metabolic transcripts in proximity to actinin-BirA*, with sarcomere transcripts being depleted.

overall_design: Streptavidin IP was conducted on day 25 iPSC-CMs followed by RNA extraction and sequencing

first: Feria

last: Ladha

first: J

middle: T


title: N7-methylguanosine tRNA modification enhances oncogenic mRNA translation and promotes intrahepatic cholangiocarcinoma progression

city: Guangzhou

first: Haining

last: Liu

address: Zhongshan road 2

institute: The first affiliated hospital of sun yat-sen university

type: Non-coding RNA profiling by high throughput sequencing

summary: The cancer cells selectively promote translation of specific oncogenic transcripts to facilitate cancer survival and progression, while the underlying mechanisms are poorly understood. N7-methylguanosine (m7G) tRNA modification and its methyltransferase complex METTL1/WDR4 are significantly up-regulated in intrahepatic cholangiocarcinoma (ICC) and associated with poor prognosis. We developed tRNA reduction and cleavage sequencing (TRAC-Seq) to reveal the m7G tRNA methylome inICC cell line and ribosome nascent-chain complex-bound mRNAs sequencing(RNC-seq) and ribosome profiling(Ribo-seq) to study the differential translated genes and reveal the ribosome pausing. A subset of 22 tRNAs is modified at a ‘RAGGU’ motif within the variable loop. We observe increased ribosome occupancy at the corresponding codons in the Mettl1 knockdown ICC cell line implying widespread effects on tRNA function, ribosome pausing, and mRNA translation. Translation of cell cycle genes and EGFR signaling pathway genes is particularly affected. Our study uncovers the important physiological function and mechanism of METTL1-mediated m7G tRNA modification in the regulation of cancer progression.

overall_design: TRAC-Seq was developed to identify the tRNA m7G methylome in the intrahepatic cholangiocarcinoma cell line. RNC-seq and Ribo-seq were used to study the differential translated genes in the Mettl1 knockdown and control cells.

first: Ming

last: Kuang


title: Differential Expression Profiles and Function Predictions for tRFs &  tiRNAs in Skin Injury Induced by Ultraviolet Irradiation

status: Public on Aug 06 2021

city: chang sha

first: yuan

last: fang

address: 138 TongZiPo road

institute: The Third Xiangya Hospital of Central South Uniiversity

summary:
Purpose: to explore the function and mechanism of skin damage induced by ultraviolet irradiation.
Method: Skin tRF & tiRNA profiles of mice normal skin and damage skin induced by Ultraviolet Irradiation (UV) were generated by deep sequencing, using Illumina NextSeq 500. qRT–PCR validation was performed using SYBR Green assays.
Results:Sequencing was used to screen expression profiles and predict target genes. Compared with normal skin, a total of 31 differentially expressed tRFs and tiRNAs were screened. Among these, 10 tRFs and tiRNAs were shown to be significantly different in expression levels, where there were 4 up-regulated and 6 down-regulated target genes.Altered expression of 4 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to skin repair after damage induced by ultraviolet irradiation.
Conclusion: tRF-Trp-TCA-001 and tRF-Gly-CCC-019 plays an important role in acute skin injury induced by UVB radiation by regulating the ras-related C3 botulinum toxin substrate 1 (Rac1) gene in the WNT signaling pathway. This study provides new insights into the mechanisms and therapeutic targets of UV-induced skin injury.

overall_design: tRF & tiRNA profiles of normal skin and UV damage skin mice

first: Yuan

last: Fang

first: Jianda

last: Zhou

first: Ke

last: Cao


title: Pam50 of a Triple-Negative Breast Cancer Cohort Treated with Neoadjuvant Carboplatin and Docetaxel According to Lehmann's Refined Classification

city: Madrid

first: Marta

last: Roche-Molina

address: C/Maiquez 7

department: Servicio de Oncologia Medica

country: Spain

institute: LAOT

summary: Our aims is correlate the data and classification of the subtype breast cancer obtained with the Pam50 assay with the data obtained from the analysis of the same patients RNAseq

overall_design: Total RNA was obtained from breast cancer tissue embedded in parafine (from the surgery) in order to perform the nanostring Pam50 assay.

first: Isabel

last: Echevarria

first: Sara

last: Lopez-Tarruella

first: Antoni

last: Picornell

first: Jose

last: Garcia-Saenz

first: Yolanda

last: Jerez

first: Katherine

last: Hoadley

first: Henry

last: Gomez

first: Fernando

last: Moreno

first: Maria

last: Del Monte-Millan

first: Ivan

last: Marquez-Rodas

first: Enrique

last: Alvarez

first: Rocio

last: Ramos-Medina

first: Javier

last: Gayarre

first: Tatiana

last: Massarrah

first: Inmaculada

last: Ocana

last: Cebollero

first: Hugo

last: Fuentes

first: Agusti

last: Barnadas

first: Ana

middle: I

last: Ballesteros

first: Uriel

last: Bohn

first: Charles

last: Perou

first: Miguel

last: Martin


title: The ETS Transcription Factor ERF Controls the Exit from the Embryonic Rosette-stage of Pluripotency [Cut&Run]

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

institute: NIH/NCI

summary: The naïve epiblast undergoes a transition to a pluripotent primed state during embryo implantation. Interestingly, a distinct intermediate stage during the naïve-to-primed transition has been recently described, the rosette stage. We propose the transcriptional repressor ERF as the MAPK-dependent switch that controls the exit from the rosette-stage of pluripotency. By using inducible ESC to genetically eliminate all RAS proteins, we show that, while differentiated RasKO ESC are reminiscent of the pluripotent rosette-stage, the absence of ERF overcomes the developmental blockage of RAS-deficient cells from this intermediate state. RNAseq data revealed that deletion of ERF restored the overall gene expression profile to a wild-type level in differentiated RasKO ESC. Mechanistically, ERF ensures naïve pluripotency by strengthening naïve pluripotent transcription factor binding and accessibility at specific ESC enhancers. Moreover, ERF regulates negatively the expression of the DNMT3 de novo methylases, which are essential for the extinction of the naïve transcriptional program. Our data revealed an essential role for ERF in the exit from rosette pluripotency as a regulator of the progression to primed pluripotency.

overall_design: Cut&Run experiments of H3K27ac, Nanog, Sox2, Otx2 in untreated and OHT-treated Raslox/lox, ERFKO, RasKO, and RasKO; ERFKO ESC cultured in naïve conditions (2iL) or induced to differentiate to EpiLSC (FA) for 48 hours.

first: Sergio

last: Ruiz

last: Vega-Sendino


title: Evalutation of DEGs by RNA-seq in panobinostat-exposed (5 mg/kg/day) embryonic murine ovary

city: Rennes

first: Fatima

last: SMAGULOVA

address: 9 av. Prof. Léon Bernard

country: France

institute: Irset - U1085

summary: We hypothesized that gestational exposure (E6.5-E15.5) to panobinostat, a HDAC inhibitor, can lead to alteration of murine ovary transcriptome.  To test our hypothesis, we exposed mice (C57Bl6j) to 5 mg/kg/day of panobinostat during embryonic development (E5.5-E15.5). Four embryonic ovaries were pooled prior RNA extraction using RNeasy Plus kit.  RNA libraries (3 control, 3 exposed) were prepared using the NEBNext Ultra II Directional RNA Library Kit for Illumina.  After pre-processing of the sequencing data we  performed an analysis of differentially expressed genes.

overall_design: For each replicate, RNA was extracted from the pool of 6 to 8 embryonic ovaries (E15.5). Three biological replicates were prepared for each condition. Stranded libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according manufacturer's instructions. Ov_RNA_Con1 : Library for exposed mouse 2 Ov_RNA_Con2 : Library for exposed mouse 3 Ov_RNA_Con3 : Library for exposed mouse 4 Ov_RNA_PB1 : Library for exposed mouse 2 Ov_RNA_PB2 : Library for exposed mouse 3 Ov_RNA_PB3 : Library for exposed mouse 4

last: Smagulova

first: Louis

last: Legoff


title: Auxin requirements for a meristematic state in roots depend on a dual brassinosteroid function

city: Haifa

first: Gur

last: Sevillya

state: Israel

address: Haifa

institute: Technion

summary: Root meristem organization is maintained by an interplay between hormone signaling pathways that both interpret and determine their accumulation and distribution. The interacting hormones Brassinosteroids (BR) and auxin control the number of meristematic cells in the Arabidopsis root. BR was reported both to promote auxin signaling input and to repress auxin signaling output. Whether these contradicting molecular outcomes co-occur and what their significance in meristem function is remain unclear. Here, we established a dual effect of BR on auxin, with BR simultaneously promoting auxin biosynthesis and repressing auxin transcriptional output, which is essential for meristem maintenance. Blocking BR-induced auxin synthesis resulted in rapid BR-mediated meristem loss. Conversely, plants with reduced BR levels were resistant to a critical loss of auxin biosynthesis, maintaining their meristem morphology. In agreement, injured root meristems, which rely solely on local auxin synthesis, regenerated when both auxin and BR synthesis were inhibited. Use of BIN2 as a tool to selectively inhibit BR signaling yielded meristems with distinct phenotypes depending on the perturbed tissue: meristem reminiscent either of BR-deficient mutants or of high BR exposure. This enabled mapping of the BR-auxin interaction that maintains the meristem to the outer epidermis and lateral root cap tissues and demonstrated the essentiality of BR signaling in these tissues for meristem response to BR. BR activity in internal tissues however, proved necessary to control BR levels. Together, we demonstrate a basis for inter-tissue coordination and how a critical ratio between these hormones determines the meristematic state.

overall_design: Arabidopsis (Arabidopsis thaliana) seedlings in the Columbia-0 (Col-0) background, were germinated on one-half-strength Murashige and Skoog medium supplemented with 0.2% (w/v) sucrose for 3 days. 3-day-old seedlings were transferred to treatments (mock, 0.8nM BL, 4 µM Kyn and their combination, and harvested after 12 h, 24 h and 48 h.Total RNA was extracted from roots. RNA sequencing and analysis were performed at the Technion Genome Center (LSE). 24 samples (2 biological replicates) were prepared using the CEL-Seq2 sample preparation protocol (Hashimshony, et al., 2016), and sequenced on a paired end run Illumina HiSeq 2500, to obtain 15 bp read 1 and 50 bp read 2.

first: Sigal

last: Savaldi-Goldstein

first: Michal

last: Ackerman-Lavert


title: Co-culture model of B-cell acute lymphoblastic leukemia recapitulates a transcription signature of chemotherapy-refractory minimal residual disease

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

summary: B-cell acute lymphoblastic leukemia (ALL) develops when immature B cells stop differentiating and begin rapidly proliferating, allowing for an accumulation of immature cells in the bone marrow as well as the periphery. The bone marrow is a well-established sanctuary site, and while standard of care treatments allows for complete remission in most patients, a small population of patients will relapse, likely due to the presence of minimal residual disease (MRD) consisting of a dormant, chemotherapy-resistant cell population. We developed an in vitro cell culture model in which human ALL cells are grown in co-culture with either bone marrow-derived stromal cells or human osteoblasts. Within this culture, tumor cells can either be found in suspension, lightly attached to the top of the adherent cells, or buried under the adherent cells in a population that is phase dim (PD) by light microscopy. We have characterized the PD cells as being both a dormant and chemo-resistant cell population that relies heavily on glycolysis for energy. Additionally, we found that this model can be used to recapitulate MRD in vitro, as a means to identify and test novel therapeutics and treatment strategies that would allow for complete eradication of the disease from the bone marrow. In the current study, we characterized the transcriptional signature of the PD cells using RNA-Seq analysis, and this data was also compared to a published data set of human MRD B-ALL patients. Our RNA-Seq analyses showed that the PD cell population from the in vitro co-culture model closely mimics MRD expression patterns in patients. These findings suggest that our in vitro system can be used as a model for mimicking MRD. Furthermore, we identified both genes and key signaling pathways that were common between the PD cells and patient MRD that can provide us with potential therapeutic targets leading to a better outcome for the subset of patients that relapse.

overall_design: REH (ATCC #CRL-8286) cell lines for ALL were grown in monoculture without bone marrow derived components (long term media culture, LTMC), co-cultured with Human osteoblasts (HOB) (PromoCell; Cat No: C-12720), or co-culutured with de-identified primary BMSCs (C2R). REH cells underneath HOB or BMSCs in co-culture (phase-dim under bright-field microscopy) were isolated (PMID: 26891147) and subjected to RNA-Seq analysis and compared to REH cultured alone.

first: Stephanie

last: Rellick

first: Debbie

last: Piktel

first: Karen

first: Werner

last: Geldenhuys

first: Raj

last: Nair

first: Laura

last: Gibson


title: Dlx1/2-Dependent Expression of Meis2 Promotes Neuronal Fate Determination in the Mammalian Striatum [CUT-Tag-seq]

city: Shanghai

first: Zihao

last: Su

address: 138 Yi Xue Yuan Road

institute: Fudan University

summary:
Purpose:To identity genomic loci where MEIS2 binds at E14.5 in the LGE
Methords:  The CUT&Tag assay was performed using E14.5 LGEs dissected from wild-type CD1 mice and a MEIS2 mouse polyclonal antibody as described previously.
Results: We derived a set of 13992 loci based on the presence of significant enrichment in MEIS2 libraries and no enrichment in the negative control datasets

first: Ziwu

last: Wang

first: Zhuangzhi

last: Zhang

first: Lin

last: Yang


title: RNAseq of a Triple-Negative Breast Cancer Cohort Treated with Neoadjuvant Carboplatin and Docetaxel According to Lehmann's Refined Classification

first: Marta

last: Roche-Molina

overall_design: Total mRNA obtained from breast cancer tissue embedded in paraffin obtained from the surgery in order to perform the RNAseq. Sample name was made using the origin place of the sample and a serial number in order to anonymize the samples (in Sample "Description" column is a condensed code with the sample name and the FFPE block number).

first: Isabel

last: Echevarria

first: Sara

last: López-Tarruella

first: Antoni

last: Picornell

first: Jose

last: García-Saenz

first: Yolanda

last: Jerez

first: Katherine

last: Hoadley

first: Henry

last: Gómez

first: Fernando

last: Moreno

first: María

last: DelMonte-Millan

first: Iván

last: Márquez-Rodas

first: Enrique

last: Alvarez

first: Rocío

last: Ramos-Medina

first: Javier

last: Gayarre

first: Tatiana

last: Massarrah

first: Inmaculada

last: Ocaña

last: Cebollero

first: Hugo

last: Fuentes

first: Agusti

last: Barnadas

first: Ana

last: Ballesteros

first: Uriel

last: Bohn

first: Charles

last: Perou

first: Miguel

last: Martin


title: Next-generation sequencing facilitates quantitative analysis of rat BMSCs in soft or stiff SA hydrogel

city: Chongqing

first: chuanchuan

last: lin

state: China

address: Shayang Road, Shapingba distract,

institute: Chongqing University

summary:
Purpose: To identify genes and the molecular pathways involved in the MSCs response to extracellular matrix stiffness, we performed RNA-sequencing of MSCs which cultured in soft (2 kPa) and stiff (18 kPa) SA hydrogels.
Methods: mRNA profiles of MSCs cultured in soft (2 kPa) and stiff (18 kPa) SA hydrogel for 48 h were generated by deep sequencing, in quadruplicate, using Illumina HiSeq 2000.
Results: Using an optimized data analysis workflow, we identified 33950 transcripts in MSCs with BWA workflow.
Conclusions: Our results present the detailed analysis of MSCs transcriptomes cultured in soft (2 kPa) and stiff (18 kPa) matrix, and found that matrix stiffness dominated multiple mRNA pathways in MSCs.

overall_design: The mRNA profiles of MSCs in soft and stiff hydrogel were generated by deep sequencing, in quadruplicate, using Illumina HiSeq 2000.

first: Kaiyong

last: Cai

first: Chuanchuan

last: Lin


title: The ETS Transcription Factor ERF Controls the Exit from the Embryonic Rosette-stage of Pluripotency [RRBS]

first: Desiree

last: Tillo

overall_design: RRBS of untreated and OHT-treated Raslox/lox, ERFKO, RasKO, and RasKO; ERFKO ESC cultured in naïve conditions (2iL) or induced to differentiate to EpiLSC (FA) for 48 hours.

first: Sergio

last: Ruiz

first: Maria

last: Vega-Sendino


title: The ETS Transcription Factor ERF Controls the Exit from the Embryonic Rosette-stage of Pluripotency [RNAseq]

overall_design: RNAseq of untreated and OHT-treated Raslox/lox, ERFKO, RasKO, and RasKO; ERFKO ESC cultured in naïve conditions (2iL) or induced to differentiate to EpiLSC (FA) for 48 hours.


title: ZC3H4 restricts non-coding transcription in human cells

city: Exeter

first: Steven

last: West

state: Devon

address: Stocker Rd

department: Living Systems Institute

institute: University of Exeter

summary: The human genome encodes many thousands of non-coding RNAs.  A majority of these are curtailed by early transcriptional termination followed by rapid degradation.  The mechanisms and factors responsible for restricting non-coding transcription in this fashion are poorly characterised, but these RNAs vastly outnumbering those with coding potential.  We identify ZC3H4 as a metazoan-specific factor controlling the level and extent of hundreds of unstable transcripts.  The most striking effects are for antisense RNAs and those transcribed from super-enhancers, but a subset of protein-coding RNAs are also affected.  ZC3H4 occupies these genomic loci and its level of recruitment correlates with RNA extension observed in its absence.  Finally, engineered targeting of ZC3H4 to an otherwise unaffected RNA supresses its production and leads to rapid degradation, endowing it with the features associated with its natural targets. We conclude that ZC3H4 is a hitherto uncharacterised factor that restricts unproductive transcription.

overall_design: Nuclear selected RNA was isolated from auxin-inducible degron (AID) tagged HCT116 cell lines treated with or without auxin, or HCT116 wild type treated with siTARGET or siCONT and sequenced using illumina total RNA sequencing. RNA Polymerase II and ZC3H4 associated DNA fragments were also analysed in the form of a ChIP-Seq experiment. We integrated an in-frame insertion of AID tag, P2A cleavage site, antibiotic resistance marker and SV40 polyA site to the 3' end of CPSF30. CPSF30-AID cells also ectopically expressed TIR1 from a sleeping beauty transposon integrated cassette. TIR1 protein is the E3 ubiquitin ligase required to induce degradation of AID containing proteins in the presence auxin.

first: Christopher

last: Estell

first: Lee

last: Davidson


title: TRIM28 is a transcriptional activator of the mutant TERT promoter in human bladder cancer

city: LOS ANGELES

first: Bassem

last: Ben Cheikh

address: 8723 Alden Drive, Suite 100

department: Biomedical Sciences

institute: CEDARS SINAI MEDICAL CENTER

summary: Human telomerase reverse transcriptase (hTERT) is a rate-limiting catalytic subunit of the enzyme telomerase, which plays a central role in maintaining replicative immortality in normal stem cells and many cancer cells. Mostly silenced in normal somatic cells, hTERT is reactivated in cancer commonly through highly recurrent hot spot point mutations in the hTERT promoter. Bladder cancer has a 60-70% hTERT promoter mutation prevalence, commonly at -124 bp from the translation start site, and this is associated with increased hTERT expression and poor patient prognosis. Identifying targetable signaling pathways that drive hTERT transcription from the mutant promoter could lead to therapies with reduced effects on normal progenitors. Here we describe a new platform that probes endogenous hTERT regulation by allele-specific insertion of GFP at either wild-type or mutant promoter allele within human bladder cancer cells harboring a heterozygous mutation. Using cells expressing the GFP-hTERT fusion protein, we performed a pooled CRISPR-Cas9 Kinome KO genetic screen to identify regulators of mutant hTERT promoter activity. We identified TRIM28 as an activator and TRIM24 as a suppressor of hTERT expression. Similar to hTERT, TRIM28 expression stratifies patient outcome and inhibits promotes cell growth both in vitro and in vivo, supporting their clinical relevance. TRIM28 and TRIM24 get recruited to the mutated promoter through GABPA, where TRIM24 interacts with TRIM28 and inhibits its activity as a transcriptional activator. TRIM28 phosphorylation causes its release from TRIM24 and activates hTERT transcription. mTOR phosphorylates TRIM28 through the mTORC1 complex leading to hTERT expression, while mTORC1 inhibition with rapamycin analog Ridaforolimus suppresses the phosphorylation and promoter binding of TRIM28, resulting in reduced hTERT expression and lower cell viability. This study uses a bespoke platform to identify a novel therapeutically tractable regulatory pathway for cancers harboring mutant hTERT promoters.

overall_design: UMG12 clone with endogenous GFP Knock-In at mutant TERT promoter allele generated from UMUC3 bladder cancer cell line was used as a model. Examination of differential gene expression after knocking down genes involved in regulating TERT expression from -124C>T mutant promoter allele.

first: Neeraj

last: Agarwal

middle: B

last: Cheikh

first: Simon

middle: R

last: Knott

first: Dan

last: Theodorescu


title: Mapping out genome wide binding sites of Prox1 by CUT&RUN approach in mouse cochlea

city: Beijing

first: Jixiang

last: Zhang

state: Beijing

address: No.1 West Beichen Road,Chaoyang District

institute: Institute of Genetics and Developmental Biology Chinese Academy of Sciences

summary: The homeobox transcription factor Prox1 is critical for organogenesis including brain, retina, liver and pancreas and lymphatic system. Prox1 is transiently expressed in mouse cochlear hair cells (HCs) and supporting cells (SCs), however, it remains elusive about its in vivo DNA binding site and roles during cochlear development. Here, by using fresh cochlear tissues and Prox1 antibody, we firstly mapped out the genome-wide binding sites of Prox1 via Cleavage Under Targets and Release Using Nuclease (CUT&RUN). Gene function enrichment analysis suggests several potential functions of Prox1, one of which is regulating cell cycle progression. Secondly, to validate our CUT&RUN data, we further performed in vivo prox1 gain-of-function studies through genetic approaches. Onset of ectopic Prox1 at early embryonic otocyst leads to shorter cochlea with density of HCs and SCs distribution, suggesting a precocious cell cycle exit of cochlear sensory progenitor cells. These findings highlight the power of CUT&RUN in mapping DNA binding sites even in tissues (i.e. cochlea) with rare cells, as well as providing the first genetic evidence to support roles of Prox1 in regulating progenitor pools of cochlear progenitors.

overall_design: Examination of Prox1 genome-wide binding sites in fresh cochlearr tissues

first: Zhennan

last: Luo


title: Long noncoding RNA SH3PXD2A-AS1 promotes NSCLC proliferation and accelerates cell cycle progression by interacting with DHX9

first: yeqing

last: zhou

address: 99 West Huaihai Road

institute: Xuzhou Medical University

summary: As the most commonly diagnosed lung cancer, non–small cell lung carcinoma (NSCLC) is regulated by many long noncoding RNAs (lncRNAs). In the present study, we found that SH3PXD2A-AS1 expression in NSCLC tissues was upregulated compared with that in normal lung tissues in The Cancer Genome Atlas (TCGA) database by using the GEPIA website. K-M analysis was performed to explore the effects of this molecule on the survival rate in NSCLC. The results demonstrated that SH3PXD2A-AS1 expression was increased in human NSCLC, and high SH3PXD2A-AS1 expression was correlated with poor overall survival. SH3PXD2A-AS1 promotes lung cancer cell proliferation and accelerates cell cycle progression in vitro. Animal studies validated that knockdown of SH3PXD2A-AS1 inhibits NSCLC cell proliferation in vivo. Mechanically, SH3PXD2A-AS1 interacted with DHX9 to enhance FOXM1 expression, promote tumour cell proliferation and accelerate cell cycle progression. Altogether, SH3PXD2A-AS1 promoted NSCLC growth by interacting with DHX9 to enhance FOXM1 expression. SH3PXD2A-AS1 may serve as a promising predictive biomarker for the diagnosis and prognosis of patients with NSCLC.

overall_design: We conducted gene expression profiling of SH3PXD2A-AS1 knockdown and vector control H292 cells in triplicate

first: Yeqing

last: Zhou

first: Hongmei

last: Yong

first: Sufang

last: Chu

first: Minle

last: Li

first: Zhongwei

first: Jin

last: Bai

first: Hao


title: Identification of regulated genes associated with ketogenic diet treatment following SCI

city: Vancouver

first: Oscar

last: Seira

state: BC

address: 818 west 10th Avenue. Blusson Spinal Cord Center. ICORD

country: Canada

institute: University of British Columbia (UBC)/ICORD

summary: To evaluate the changes in gene expression after spinal cord injury (SCI) and treatment with a Ketogenic Diet or a Control Diet (Refs., CD: F5960, Bioserv®; KD: F5848, Bioserv®), gene expression was studied 7 days after SCI surgery in rats. A total of 8 adult male Sprague-Dawley rats (~300 g at time of injury; Harlan Breeding Laboratory) were group-housed (21°C; 12 h: 12 h light:dark cycle). After a unilateral C5 laminectomy -dorsal processes of C4-C6 were held with a clamp and fixed in a frame tilted at a 22.5° angle and the cord was consutesd with a force of 150 Kdynes using the Infinite Horizon impactor- the animals were given ad libitum access to the 2 diets. Total RNA was isolated from 5-mm segment centered on the site of impact.

overall_design: Changes in gene expression in injured spinal cords were measured at 1 week post injury after the animals were fed ad libitum with either a tandard or Control Diet (SD) or a Ketogenic Diet (KD)  for the entire length of the experiment.

first: Femke

last: Streijger

first: Wolfram

last: Tetzlaff


title: Large-scale Chemical Screen Identifies a Geroprotective Role of Gallic Acid in Premature Aging [ATAC-seq]

status: Public on Aug 05 2021

first: jiang

middle: xiao

last: yu

address: 15 Datun Road Chaoyang District

institute: institute of zoology, CAS

summary: Gallic acid (GA) is a natural phenolic compound with antioxidant, anti-inflammatory, and antineoplastic  properties. Previous studies also revealed that GA supplementation inhibit the decline of rat embryonic and rejuvenate the immune function in D-gal-induced aging accelerated mice. However, the role of GA in regulating senescence of human premature aging stem cells is unknown. We have demonstrated that GA showed beneficial effects in alleviating human mesenchymal stem cell (hMSC) senescence: (1) GA alleviated senescence by promoting stem cell self-renewal ability and down-regulating the expression of aging markers, including P16 and P21, in Werner syndrome (WS) hMSCs; (2) High levels of reactive oxygen species in total cell as well as mitochondria were both rescued by GA treatment; (3) GA also maintained epigenetic features, enhanced cell stemness, and improved mitochondrial homeostasis in WS hMSCs. Our data provide substantial evidence supporting that GA is a promising candidate agent to

overall_design: ATAC sequencing in Werner syndrome (WS) hMSCs, DMSO-treated cells, GA (gallic acid)-treated cells.

first: Guanghui

last: Liu


title: Single-cell transcriptome profiling reveals the suppressive role of retinal neurons in microglia activation under diabetes mellitus

city: guangzhou

first: yuhua

last: xiao

state: guangdong province

address: jinsui load

department: zhongshan Ophthalmic  center

institute: Sun Yat-sen University

summary: Diabetic retinopathy, as one of the common complications of diabetes mellitus, is the leading cause of blindness in working-age population. The disease is characterized by damage to retinal vasculature, which is associated with the activation of retina microglial and chronic neurodegeneration. Previous studies have identified the effects of activated microglial on the retinal neurons, but how the microglial activation is regulated by the others is largely unknown. Here, we performed scRNA-seq on the retina of non-human primates with diabetes mellitus, and identified cell-type-specific molecular changes of the six major cell types. By identifying the ligand-receptor expression patterns among different cells, we established the interactome of the whole retina. The data showed that TNF-α signal mediated the activation of microglial through an autocrine manner. We found Muller and amacrine acted through SPP1 signaling and cone acted through TGFβ signaling, to inhibit the genes related to microglial activation. Our study is the first to profile cell-specific molecular changes and the cell-cell interactome of retina under diabetes mellitus, paving a way to dissect the cellular and molecular mechanisms underlying early-stage diabetic retinopathy.

overall_design: scRNA-seq profiles of retina from control and diabetes mellitus.

first: Yuhua

last: Xiao


title: CD8 response to checkpoint immunohterapy in kidney cancer patients

city: Atlanta

first: Haydn

last: Kissick

address: 1462 Clifton Rd.

institute: Emory University

summary: This study isolated activated CD8 cells from kidney cancer patients undergoing checkpoint immunotherapy before treatemnt and after the first and second cycles of treatment

overall_design: baseline, cycle 1 and cycle 2 blood were collected from 25 kidney cancer patients receiving checkpoint immunotherapy


title: MicroRNAs and tRNA fragments as biomarkers of chondrosarcoma and Paget's disease of bone

status: Public on Aug 13 2021

city: Norwich

first: Darrell

last: Green

address: Earlham Road

department: Norwich Medical School

institute: University of East Anglia

summary: We extracted total RNA from fingerstick samples of normal, chondrosarcoma and Paget's disease patients. We then constructed small RNA libraries using HD adapters in order to identify small RNA biomarkers

overall_design: By comparing the blood profiles of normal and disease patients, we aimed to identify an appropriate biomarker for clinical diagnostic use

first: Irina

last: Mohorianu

first: Laura

last: Bird

first: Tamas

last: Dalmay

first: William

last: Fraser


title: Large-scale Chemical Screen Identifies a Geroprotective Role of Gallic Acid in Premature Aging

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: NADPH oxidase 4 (Nox4) deletion accelerates liver regeneration in mice

city: L'Hospitalet de Llobregat

first: ISABEL

last: FABREGAT ROMERO

state: Barcelona

address: Avinguda de la Granvia de l’Hospitalet, 199

department: Oncobell Program

institute: Bellvitge Biomedical Research Institute - IDIBELL

summary: RNA-seq analysis was performed in samples from WT and NOX4 Knock-out mice after two-thirds Partial Hepatectomy (PH). Transcriptomic analysis through RNA-seq revealed significant changes mainly 24 hours after PH in NOX4-/- mice and support a relevant role for Myc in a node of regulation of proliferation-related genes.

overall_design: Two-thirds Partial Hepatectomy was performed in WT and NOX4 Knock-out mice and samples were collected at different time points after the surgeries. Liver mRNA samples were obtained and RNA-seq was performed.

first: Macarena

last: Herranz-Itúrbide

first: Judit

last: López-Luque

first: Ester

last: Gonzalez-Sanchez

first: Daniel

last: Caballero-Díaz

first: Eva

last: Crosas-Molist

first: Beatriz

last: Martín-Mur

first: Marta

last: Gut

first: Anna

last: Esteve-Codina

first: Vincent

last: Jaquet

first: Joy

middle: X

last: Jiang

first: Natalie

last: Török

first: Isabel

last: Fabregat